Variant 7-144399505-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001080413.3(NOBOX):c.1155-23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 1,547,152 control chromosomes in the GnomAD database, including 278,790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 28922 hom., cov: 33)

Exomes 𝑓: 0.59 ( 249868 hom. )

Consequence

NOBOX
NM_001080413.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.00

Variant links:

Genes affected

NOBOX (HGNC:22448): (NOBOX oogenesis homeobox) This homeobox gene encodes a transcription factor that is thought to play a role in oogenesis. In mice, it is essential for folliculogenesis and regulation of oocyte-specific genes. Defects in this gene result in premature ovarian failure type 5.[provided by RefSeq, May 2011]

NOBOX links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 7-144399505-C-T is Benign according to our data. Variant chr7-144399505-C-T is described in ClinVar as [Benign]. Clinvar id is 1222892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOBOX	NM_001080413.3 linkuse as main transcript	c.1155-23G>A		intron_variant		ENST00000467773.1	NP_001073882.3
NOBOX	XM_017011742.3 linkuse as main transcript	c.1059-23G>A		intron_variant			XP_016867231.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
NOBOX	ENST00000467773.1 linkuse as main transcript	c.1155-23G>A	intron_variant	5	NM_001080413.3	ENSP00000419457		O60393-1
NOBOX	ENST00000483238.5 linkuse as main transcript	c.1059-23G>A	intron_variant	5		ENSP00000419565	A2	O60393-2
NOBOX	ENST00000643164.1 linkuse as main transcript	c.252-23G>A	intron_variant			ENSP00000495343
NOBOX	ENST00000645489.1 linkuse as main transcript	c.804-23G>A	intron_variant			ENSP00000496732	P2

Frequencies

GnomAD3 genomes

AF:

0.612

AC:

93007

AN:

151964

Hom.:

28892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.645

Gnomad AMI

AF:

0.656

Gnomad AMR

AF:

0.620

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.829

Gnomad SAS

AF:

0.831

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.618

GnomAD3 exomes

AF:

0.639

AC:

106092

AN:

165984

Hom.:

34737

AF XY:

0.648

AC XY:

56932

AN XY:

87874

show subpopulations

Gnomad AFR exome

AF:

0.656

Gnomad AMR exome

AF:

0.650

Gnomad ASJ exome

AF:

0.599

Gnomad EAS exome

AF:

0.821

Gnomad SAS exome

AF:

0.799

Gnomad FIN exome

AF:

0.535

Gnomad NFE exome

AF:

0.578

Gnomad OTH exome

AF:

0.607

GnomAD4 exome

AF:

0.594

AC:

828797

AN:

1395070

Hom.:

249868

Cov.:

AF XY:

0.601

AC XY:

414465

AN XY:

689716

show subpopulations

Gnomad4 AFR exome

AF:

0.646

Gnomad4 AMR exome

AF:

0.643

Gnomad4 ASJ exome

AF:

0.604

Gnomad4 EAS exome

AF:

0.786

Gnomad4 SAS exome

AF:

0.798

Gnomad4 FIN exome

AF:

0.528

Gnomad4 NFE exome

AF:

0.571

Gnomad4 OTH exome

AF:

0.618

GnomAD4 genome

AF:

0.612

AC:

93089

AN:

152082

Hom.:

28922

Cov.:

AF XY:

0.617

AC XY:

45871

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.645

Gnomad4 AMR

AF:

0.620

Gnomad4 ASJ

AF:

0.606

Gnomad4 EAS

AF:

0.828

Gnomad4 SAS

AF:

0.832

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.569

Gnomad4 OTH

AF:

0.623

Alfa

AF:

0.599

Hom.:

4684

Bravo

AF:

0.615

Asia WGS

AF:

0.812

AC:

2821

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -

Premature ovarian failure 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.46

DANN

Benign

0.63

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over